Cannot run Shiny app on Rackham.
Error:
Warning: Error in Cairo: X11 fatal IO error: please save work and shut down R
Full error log:
(firefox:9429): dconf-CRITICAL **: 00:53:25.200: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.200: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.201: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.201: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.214: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.215: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.215: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.216: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.217: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.217: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.218: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
[Parent 9429, Main Thread] WARNING: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.: 'glib warning', file /builddir/build/BUILD/firefox-115.11.0/toolkit/xre/nsSigHandlers.cpp:167
(firefox:9429): dconf-CRITICAL **: 00:53:25.218: unable to create directory '/run/user/4014270/dconf': Permission denied. dconf will not work properly.
Warning: Error in Cairo: X11 fatal IO error: please save work and shut down R
132: Cairo
131: <Anonymous>
129: startPNG
128: drawPlot
114: <reactive:plotObj>
98: drawReactive
85: renderFunc
84: output$ATAC
3: shiny::runApp
2: shiny::runGadget
1: ArchRBrowser
[ERROR viaduct::backend::ffi] Missing HTTP status
[ERROR viaduct::backend::ffi] Missing HTTP status
[ERROR viaduct::backend::ffi] Missing HTTP status
From https://mastering-shiny.org/basic-app.html created
library(shiny)
ui <- fluidPage(
"Hello, world!"
)
server <- function(input, output, session) {
}
shinyApp(ui, server)and put this in app.R
Testing this on a local Ubuntu 24.04 Nimble computer:
Works!
Following the doc at https://docs.uppmax.uu.se/getting_started/login_rackham_remote_desktop_website/, browse to https://rackham-gui.uppmax.uu.se/.
Starting an interactive node, from the doc at https://docs.uppmax.uu.se/cluster_guides/start_interactive_node_on_rackham/:
interactive -A staffThen, from https://docs.uppmax.uu.se/cluster_guides/rstudio_on_rackham/:
module load RStudio/2023.06.2-561Gives the new RStudio error:
[richel@r486 richel]$ module load RStudio/2023.06.2-561
RStudio/2023.06.2-561: Sandboxing is not enabled for RStudio at UPPMAX. See 'module help RStudio/2023.06.2-561' for more information
Doing that:
[richel@r486 richel]$ module help RStudio/2023.06.2-561
------------------------------------------------------------------- Module Specific Help for "RStudio/2023.06.2-561" -------------------------------------------------------------------
RStudio - use RStudio 2023.06.2-561
Version 2023.06.2-561
With the Linux distribution used on most UPPMAX clusters (CentOS 7), RStudio/2023.06.2-561
prefers to use a 'suid sandbox'. We do not enable this at UPPMAX. Instead, we disable sandboxing
during startup of RStudio by defining a shell alias for the 'rstudio' command. You may notice
additional errors in the terminal window from which you ran the 'rstudio' command. This is
expected and does not affect RStudio operation.
For performance reasons, UPPMAX disables checks for updates.
UPPMAX also disables the 'Packages' pane of RStudio if an R_packages module is loaded.
So, starting with:
rstudioThen in a terminal:
wget https://raw.githubusercontent.com/uppsala-makerspace/ticket_295455/main/app.RIn RStdio loading the code works fine. It asks for installing the Shiny package. I clicked 'Yes'
After about 5-10 minutes, the application starts:
The output my terminal gave was:
[richel@r486 richel]$ rstudio
[18024:0726/104545.209328:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104545.209673:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104546.373753:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104546.737316:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18079:0726/104546.902133:ERROR:gpu_memory_buffer_support_x11.cc(49)] dri3 extension not supported.
[18024:0726/104546.946939:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104552.518751:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104552.623480:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104552.700426:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104552.798535:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104552.854285:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104552.973297:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104553.128395:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104553.283083:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104553.528514:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104553.620319:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104557.382935:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18079:0726/104725.557888:ERROR:x11_software_bitmap_presenter.cc(142)] XGetWindowAttributes failed for window 48234522
[18024:0726/104730.716378:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104737.106778:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104737.502709:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104737.778362:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104737.941378:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104738.022613:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104738.091062:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104738.314841:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104738.557383:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104747.493216:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/104753.408875:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105345.083508:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105346.021231:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105347.979216:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105347.987551:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.093490:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.095120:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.151288:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.152771:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.225266:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.230389:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.392199:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105348.396476:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105353.207382:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
[18024:0726/105353.210750:ERROR:bus.cc(399)] Failed to connect to the bus: Failed to connect to socket /tmp/dbus-3OPAsJRfcJ: Connection refused
so apparently, these are not a problem.